We present preliminary results for the axial, scalar and tensor charges of the nucleon measured in 2+1 flavor QCD with the physical light quarks (m π = 135 MeV). Our simulations are carried out with gauge configurations generated by the PACS Collaboration with the stout-smeared O(a) improved Wilson fermions and Iwasaki gauge action at a single lattice spacing of 0.085 (fm). There are two lattice ensembles of the PACS gauge configurations, which have physical lattice sizes over (10 fm) 4 and (5 fm) 4 , respectively. We compute the nucleon three-point correlation functions in the axial, scalar, and tensor channels. For the renormalization, we use the Rome-Southampton method as the intermediate scheme in order to evaluate the renormalization constants for the scalar and tensor currents in fully nonperturbative manner. We then evaluate the renormalized values of the scalar and tensor charges (g S and g T ) in the MS scheme at the renormalization scale of 2 GeV with a help of the continuum perturbation theory for the matching between two schemes. We compare our preliminary results of g S and g T with those of other collaboration results.